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RNA-Seq for Gene Expression Profiling of Human Necrotizing Enterocolitis: a Pilot Study

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ABSTRACT

Necrotizing enterocolitis (NEC) characterized by inflammatory intestinal necrosis is a major cause of mortality and morbidity in newborns. Deep RNA sequencing (RNA-Seq) has recently emerged as a powerful technology enabling better quantification of gene expression than microarrays with a lower background signal. A total of 10 transcriptomes from 5 pairs of NEC lesions and adjacent normal tissues obtained from preterm infants with NEC were analyzed. As a result, a total of 65 genes (57 down-regulated and 8 up-regulated) revealed significantly different expression levels in the NEC lesion compared to the adjacent normal region, based on a significance at fold change ≥ 1.5 and P ≤ 0.05. The most significant gene, DPF3 (P < 0.001), has recently been reported to have differential expressions in colon segments. Our gene ontology analysis between NEC lesion and adjacent normal tissues showed that down-regulated genes were included in nervous system development with the most significance (P = 9.3 × 10−7; Pcorr = 0.0003). In further pathway analysis using Pathway Express based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, genes involved in thyroid cancer and axon guidance were predicted to be associated with different expression (Pcorr = 0.008 and 0.020, respectively). Although further replications using a larger sample size and functional evaluations are needed, our results suggest that altered gene expression and the genes' involved functional pathways and categories may provide insight into NEC development and aid in future research.

No MeSH data available.


Related in: MedlinePlus

NEC tissues for experiment and histological features. Arrows indicate 2 tissue sections (NEC lesion and adjacent normal regions) from the resected small bowel segment and each histological examination.NEC = necrotizing enterocolitis.
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Figure 1: NEC tissues for experiment and histological features. Arrows indicate 2 tissue sections (NEC lesion and adjacent normal regions) from the resected small bowel segment and each histological examination.NEC = necrotizing enterocolitis.

Mentions: A total of 5 NEC patients, with median gestational ages of 26 weeks and 2 days, birth weight of 922 g, and birth height of 34.2 cm, were enrolled in this study. None of the patients showed other congenital anomalies in the perinatal period, and the mothers had no antenatal/perinatal problems except for premature delivery. The exploratory laparotomy was performed in the NEC patients at a median gestational age of 29 weeks and 1 day. The operations included a segmental resection with temporary ileostomy or primary anastomosis. All patients recovered from NEC and survived without complications. Following surgery, a histological examination of NEC lesion and adjacent normal tissues from the patients was performed (Fig. 1).


RNA-Seq for Gene Expression Profiling of Human Necrotizing Enterocolitis: a Pilot Study
NEC tissues for experiment and histological features. Arrows indicate 2 tissue sections (NEC lesion and adjacent normal regions) from the resected small bowel segment and each histological examination.NEC = necrotizing enterocolitis.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5383615&req=5

Figure 1: NEC tissues for experiment and histological features. Arrows indicate 2 tissue sections (NEC lesion and adjacent normal regions) from the resected small bowel segment and each histological examination.NEC = necrotizing enterocolitis.
Mentions: A total of 5 NEC patients, with median gestational ages of 26 weeks and 2 days, birth weight of 922 g, and birth height of 34.2 cm, were enrolled in this study. None of the patients showed other congenital anomalies in the perinatal period, and the mothers had no antenatal/perinatal problems except for premature delivery. The exploratory laparotomy was performed in the NEC patients at a median gestational age of 29 weeks and 1 day. The operations included a segmental resection with temporary ileostomy or primary anastomosis. All patients recovered from NEC and survived without complications. Following surgery, a histological examination of NEC lesion and adjacent normal tissues from the patients was performed (Fig. 1).

View Article: PubMed Central - PubMed

ABSTRACT

Necrotizing enterocolitis (NEC) characterized by inflammatory intestinal necrosis is a major cause of mortality and morbidity in newborns. Deep RNA sequencing (RNA-Seq) has recently emerged as a powerful technology enabling better quantification of gene expression than microarrays with a lower background signal. A total of 10 transcriptomes from 5 pairs of NEC lesions and adjacent normal tissues obtained from preterm infants with NEC were analyzed. As a result, a total of 65 genes (57 down-regulated and 8 up-regulated) revealed significantly different expression levels in the NEC lesion compared to the adjacent normal region, based on a significance at fold change ≥ 1.5 and P ≤ 0.05. The most significant gene, DPF3 (P < 0.001), has recently been reported to have differential expressions in colon segments. Our gene ontology analysis between NEC lesion and adjacent normal tissues showed that down-regulated genes were included in nervous system development with the most significance (P = 9.3 × 10−7; Pcorr = 0.0003). In further pathway analysis using Pathway Express based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, genes involved in thyroid cancer and axon guidance were predicted to be associated with different expression (Pcorr = 0.008 and 0.020, respectively). Although further replications using a larger sample size and functional evaluations are needed, our results suggest that altered gene expression and the genes' involved functional pathways and categories may provide insight into NEC development and aid in future research.

No MeSH data available.


Related in: MedlinePlus